rs3814526

Variant names:

• chr9-128148408-A-G
• rs3814526

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0761 in 152,254 control chromosomes in the GnomAD database, including 858 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.076 (858 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0762 AC: 11594 AN: 152136 Hom.: 861 Cov.: 31

Gnomad AFR AF: 0.0935

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0840

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0689

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0761 AC: 11584 AN: 152254 Hom.: 858 Cov.: 31 AF XY: 0.0799 AC XY: 5947 AN XY: 74438

African (AFR) AF: 0.0933 AC: 3878 AN: 41548

American (AMR) AF: 0.0527 AC: 806 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3468

East Asian (EAS) AF: 0.438 AC: 2264 AN: 5166

South Asian (SAS) AF: 0.106 AC: 514 AN: 4828

European-Finnish (FIN) AF: 0.0840 AC: 891 AN: 10606

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2958 AN: 68020

Other (OTH) AF: 0.0687 AC: 145 AN: 2112

Alfa AF: 0.0558 Hom.: 2141

Bravo AF: 0.0766

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.59
PhyloP100		1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3814526; hg19: chr9-130910687;